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Information on EC 3.2.1.55 - non-reducing end alpha-L-arabinofuranosidase and Organism(s) Geobacillus stearothermophilus and UniProt Accession Q9XBQ3

for references in articles please use BRENDA:EC3.2.1.55
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IUBMB Comments
The enzyme acts on alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)- and/or (1,5)-linkages, arabinoxylans and arabinogalactans. Some beta-galactosidases (EC 3.2.1.23) and beta-D-fucosidases (EC 3.2.1.38) also hydrolyse alpha-L-arabinosides. cf. EC 3.2.1.185, non-reducing end beta-L-arabinofuranosidase.
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This record set is specific for:
Geobacillus stearothermophilus
UNIPROT: Q9XBQ3
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The taxonomic range for the selected organisms is: Geobacillus stearothermophilus
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
arabinofuranosidase, arabinosidase, alpha-l-araf, alpha-arabinosidase, alpha-l-arabinosidase, afase, alpha-l-arabinofuranosidase b, arabinoxylan arabinofuranohydrolase, alpha-araf, alpha-arabinofuranosidase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
alpha-L-arabinofuranosidase
-
ABF
-
-
-
-
alpha-arabinofuranosidase
-
-
-
-
alpha-arabinosidase
-
-
-
-
Alpha-L-AF
-
-
-
-
alpha-L-arabinanase
-
-
-
-
alpha-L-arabinofuranosidase
-
-
alpha-L-arabinofuranoside hydrolase
-
-
-
-
alpha-L-arabinosidase
-
-
-
-
arabinosidase
-
-
-
-
L-arabinosidase
-
-
-
-
polysaccharide alpha-L-arabinofuranosidase
-
-
-
-
additional information
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of O-glycosyl bond
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
alpha-L-arabinofuranoside non-reducing end alpha-L-arabinofuranosidase
The enzyme acts on alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)- and/or (1,5)-linkages, arabinoxylans and arabinogalactans. Some beta-galactosidases (EC 3.2.1.23) and beta-D-fucosidases (EC 3.2.1.38) also hydrolyse alpha-L-arabinosides. cf. EC 3.2.1.185, non-reducing end beta-L-arabinofuranosidase.
CAS REGISTRY NUMBER
COMMENTARY hide
9067-74-7
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2',4',6'-trichlorophenyl alpha-L-arabinofuranoside + H2O
2',4',6'-trichlorophenol + alpha-L-arabinofuranose
show the reaction diagram
-
-
-
?
2',4',6'-trichlorophenyl alpha-L-arabinofuranoside + H2O
2,4,6-trichlorophenol + alpha-L-arabinofuranose
show the reaction diagram
-
-
-
r
2',5'-dinitrophenyl alpha-L-arabinofuranoside + H2O
2,5-dinitrophenol + alpha-L-arabinofuranose
show the reaction diagram
-
-
-
r
2,5-dinitrophenyl-alpha-L-arabinofuranoside + H2O
2,5-dinitrophenol + L-arabinofuranose
show the reaction diagram
-
-
-
?
3',4''-dinitrophenyl alpha-L-arabinofuranoside + H2O
3',4''-dinitrophenol + alpha-L-arabinofuranose
show the reaction diagram
-
-
-
?
3',4'-dinitrophenyl alpha-L-arabinofuranoside + H2O
3',4'-dinitrophenol + alpha-L-arabinofuranose
show the reaction diagram
-
-
-
r
3-nitrophenyl-alpha-L-arabinofuranoside + H2O
3-nitrophenol + alpha-L-arabinofuranose
show the reaction diagram
-
-
-
r
4-nitrophenyl alpha-L-arabinofuranoside + H2O
4-nitrophenol + alpha-L-arabinofuranose
show the reaction diagram
-
-
-
r
m-nitrophenyl-alpha-L-arabinofuranoside + H2O
m-nitrophenol + L-arabinofuranose
show the reaction diagram
-
-
-
?
2,5-dinitrophenyl beta-D-xylopyranoside + H2O
2,5-dinitrophenol + beta-D-xylopyranose
show the reaction diagram
-
-
-
-
?
2-nitrophenyl beta-D-xylopyranoside + H2O
2-nitrophenol + beta-D-xylopyranose
show the reaction diagram
-
-
-
-
?
3,4-dinitrophenyl beta-D-xylopyranoside + H2O
3,4-dinitrophenol + beta-D-xylopyranose
show the reaction diagram
-
-
-
-
?
arabinoxylan + H2O
L-arabinose + D-xylose
show the reaction diagram
-
-
-
-
?
beet arabinan + H2O
L-arabinose + ?
show the reaction diagram
carboxymethyl cellulose + H2O
?
show the reaction diagram
-
-
-
-
?
L-arabinan + H2O
(1,5-alpha-L-arabinose)25 + ?
show the reaction diagram
-
-
-
-
?
L-arabinogalactan + H2O
L-arabinose + ?
show the reaction diagram
L-arabinoxylan + H2O
L-arabinose + ?
show the reaction diagram
oat spelt xylan + H2O
L-arabinose + ?
show the reaction diagram
-
-
-
-
?
p-nitrophenyl-alpha-L-arabinofuranoside + H2O
p-nitrophenol + alpha-L-arabinofuranose
show the reaction diagram
-
-
-
-
?
p-nitrophenyl-alpha-L-arabinofuranoside + H2O
p-nitrophenol + L-arabinose
show the reaction diagram
-
-
-
-
?
phenyl alpha-L-arabinofuranoside + H2O
L-arabinose + phenol
show the reaction diagram
-
-
-
-
ir
softwood Kraft pulp + H2O
lignin + ?
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
arabinoxylan + H2O
L-arabinose + D-xylose
show the reaction diagram
-
-
-
-
?
beet arabinan + H2O
L-arabinose + ?
show the reaction diagram
oat spelt xylan + H2O
L-arabinose + ?
show the reaction diagram
-
-
-
-
?
p-nitrophenyl-alpha-L-arabinofuranoside + H2O
p-nitrophenol + alpha-L-arabinofuranose
show the reaction diagram
-
-
-
-
?
softwood Kraft pulp + H2O
lignin + ?
show the reaction diagram
-
-
-
-
?
additional information
?
-
key enzyme in the complete degradation of the plant cell wall, enzyme is a hemicellulose, probable mechanistic pathway
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Sodium azide
activates the wild-type enzyme over 40fold
Mg2+
-
small stimulating effect
Mn2+
-
small stimulating effect
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3',4'-dinitrophenyl alpha-L-arabinofuranoside
uncompetitive substrate inhibition occurs at high concentrations
3-nitrophenyl-alpha-L-arabinofuranoside
uncompetitive substrate inhibition occurs at high concentrations
Fe2+
-
1 mM FeSO4 inhibits the activity by 25%
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
beta-xylosidase
-
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.01 - 0.53
2',4',6'-trichlorophenyl alpha-L-arabinofuranoside
0.003 - 0.35
2',5'-dinitrophenyl alpha-L-arabinofuranoside
0.6 - 1.7
3-nitrophenyl-alpha-L-arabinofuranoside
0.14 - 0.65
4-nitrophenyl-alpha-L-arabinofuranoside
0.1 - 8
2,5-dinitrophenyl beta-D-xylopyranoside
5.3 - 15.3
2-nitrophenyl beta-D-xylopyranoside
0.9 - 4.4
3,4-dinitrophenyl beta-D-xylopyranoside
0.22 - 0.42
p-nitrophenyl-alpha-L-arabinofuranoside
additional information
additional information
detailed kinetic study, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.24 - 65
2',4',6'-trichlorophenyl alpha-L-arabinofuranoside
0.72 - 190
2',5'-dinitrophenyl alpha-L-arabinofuranoside
0.66 - 340
3',4'-dinitrophenyl alpha-L-arabinofuranoside
0.0041 - 83
3-nitrophenyl-alpha-L-arabinofuranoside
0.08 - 87
4-nitrophenyl-alpha-L-arabinofuranoside
additional information
additional information
kcat with mutant 294A
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
12
3',4'-dinitrophenyl alpha-L-arabinofuranoside
pH 6.0, 40°C, wild-type enzyme
10
3-nitrophenyl-alpha-L-arabinofuranoside
pH 6.0, 40°C, wild-type enzyme
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
126
-
purified enzyme
95
-
extracellular enzyme activity
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
IABF_GEOSE
502
0
57212
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
57218
6 * 57218, calculated from sequence
108000
-
gel filtration, Sepharose Cl 6B
110000
-
gel filtration
114800
-
gel filtration, Superose 12
190000
-
gel filtration
284000
52500
-
1 * 52500 + 1 * 57500, SDS-PAGE
57500
-
1 * 52500 + 1 * 57500, SDS-PAGE
64000
-
4 * 64000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
dimer
tetramer
additional information
each subunit is composed of 2 domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native and selenomethionine-labeled wild-type enzyme, and mutant E175A in complex with substrates arabinofuranose, Ara-alpha(1-3)-Xyl and 4-nitrophenyl-Ara, from 23% w/v PEG 3350, 0.2 M NH4F, 5% v/v 2-propanol, 0.1 M Tris-HCl, pH 8.0, complex formation by soaking of crystals at 4°C in a cryo-solution containing additionally 12% glycerol and 20 mM of the substrate compounds, X-ray diffraction structure determination and analysis at 1.2-2.1 A resolution, modeling
recombinant native and selenomethionine-containing enzyme are crystallized by the sitting-drop method at 20°C in two different space groups, P2(1) with unit-cell parameters a = 100.8, b = 178.1, c = 196.2 A, beta = 96.1° and R3 with unit-cell parameters a = b = 179.3, c = 100.4 A. The R3 crystals diffract X-rays to a resolution of 1.8 A
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E175A
site-directed mutagenesis, altered kinetic properties
E294A
site-directed mutagenesis, reduced activity and about 10fold increased Km for substrate 2',4',6'-trichlorophenyl alpha-L-arabinofuranoside compared to the wild-type enzyme
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60 - 80
-
at pH 7 enzyme is completely stable at 60°C for at least 80 min, retains 50% of its maximum activity after 75 min at 70°C and loses all activity after 15 min at 80°C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
about 6 h half-life of the enzyme at 60°C
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
method not mentioned
-
recombinant enzyme, expressed in Escherichia coli BL21(DE3)
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
overexpression of wild-type and mutant enzymes in Escherichia coli BL21(DE3)
cloning of the abfA T-6 gene, PCR, T7 polymerase expression vector pET9d, expressed in Escherichia coli BL21(DE3)
-
expressed in Escherichia coli
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
agriculture
-
bioconversion of lignocellulose material for the improvement of animal feedstock digestibility
nutrition
-
aromatic potential in wine, exploitation in flavor improvement and wine aromatization
paper production
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Bezalel, L.; Shoham, Y.; Rosenberg, E.
Characterization and delignification activity of a thermostable alpha-L-arabinofuranosidase from Bacillus stearothermophilus
Appl. Microbiol. Biotechnol.
40
57-62
1993
Aspergillus niger, Geobacillus stearothermophilus, Geobacillus stearothermophilus L1
-
Manually annotated by BRENDA team
Gilead, S.; Shoham, Y.
Purification and characterization of alpha-L-arabinofuranosidase from Bacillus stearothermophilus T-6
Appl. Environ. Microbiol.
61
170-174
1995
Aspergillus niger, Butyrivibrio fibrisolvens, Butyrivibrio fibrisolvens GS113, Clostridium acetobutylicum, Geobacillus stearothermophilus, Geobacillus stearothermophilus L1, Geobacillus stearothermophilus T-6, Ruminococcus albus, Ruminococcus albus 8, Sclerotinia sclerotiorum, Streptomyces diastaticus, Streptomyces lividans, Streptomyces lividans 66, Streptomyces lividans 66 1326, Streptomyces purpurascens, Trichoderma reesei
Manually annotated by BRENDA team
Schwarz, W.H.; Bronnenmeier, K.; Krause, B.; Lottspeich, F.; Staudenbauer, W.L.
Debranching of arabinoxylan: Properties of the thermoactive recombinant alpha-L-arabinofuranosidase from Clostridium stercoarium (ArfB)
Appl. Microbiol. Biotechnol.
43
856-860
1995
Aspergillus niger, Butyrivibrio fibrisolvens, Butyrivibrio fibrisolvens GS113, Geobacillus stearothermophilus, Ruminococcus albus, Ruminococcus albus 8, Streptomyces purpurascens, Thermoclostridium stercorarium
Manually annotated by BRENDA team
Debeche, T.; Cummings, N.; Connerton, I.; Debeire, P.; O'Donohue, M.J.
Genetic and biochemical characterization of a highly thermostable alpha-L-arabinofuranosidase from Thermobacillus xylanilyticus
Appl. Environ. Microbiol.
66
1734-1736
2000
Aspergillus awamori, Aspergillus awamori IFO 4033, Aspergillus niger, Aspergillus terreus, Aureobasidium pullulans, Bacillus subtilis, Bacillus subtilis 03. Jun, Bifidobacterium adolescentis, Breznakibacter xylanolyticus, Geobacillus stearothermophilus, Raphanus sativus, Streptomyces lividans, Streptomyces lividans 66 1326, Streptomyces purpurascens, Thermobacillus xylanilyticus, Thermobacillus xylanilyticus D3, Thermoclostridium stercorarium
Manually annotated by BRENDA team
Yanai, T.; Sato, M.
Purification and characterization of a novel alpha-L-arabinofuranosidase from Pichia capsulata X91
Biosci. Biotechnol. Biochem.
64
1181-1188
2000
Aspergillus awamori, Aspergillus awamori IFO 4033, Aspergillus niger, Aspergillus terreus, Aspergillus terreus CECT 2663, Aureobasidium pullulans, Butyrivibrio fibrisolvens, Butyrivibrio fibrisolvens GS113, Clostridium acetobutylicum, Dichomitus squalens, Geobacillus stearothermophilus, Geobacillus stearothermophilus T-6, Kuraishia capsulata, Kuraishia capsulata X91, Rhodotorula flava, Scopolia japonica, Streptomyces diastaticus
Manually annotated by BRENDA team
Lee, R.C.; Burton, R.A.; Hrmova, M.; Fincher, G.B.
Barley arabinoxylan arabinofuranohydrolases: Purification, characterization and determination of primary structures from cDNA clones
Biochem. J.
356
181-189
2001
Arabidopsis thaliana, Geobacillus stearothermophilus, Bacillus subtilis, Bacillus sp. (in: Bacteria), Breznakibacter xylanolyticus, Hordeum vulgare, Streptomyces coelicolor, Thermotoga maritima, Thermoclostridium stercorarium (O08457), Aspergillus niger (P42254), Streptomyces chartreusis (P82593), Bacteroides ovatus (Q59218)
Manually annotated by BRENDA team
Beylot, M.H.; Emani, K.; McKie, V.A.; Gilbert, H.J.; Pell, G.
Pseudomonas cellulosa expresses a single membrane-bound glycoside hydrolase family 51 arabinofuranosidase
Biochem. J.
385
599-605
2001
Geobacillus stearothermophilus, Cellvibrio japonicus, Streptomyces chartreusis
-
Manually annotated by BRENDA team
Shallom, D.; Belakhov, V.; Solomon, D.; Gilead-Gropper, S.; Baasov, T.; Shoham, G.; Shoham, Y.
The identification of the acid-base catalyst of alpha-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase
FEBS Lett.
514
163-167
2002
Agrobacterium tumefaciens, Bacillus subtilis, Geobacillus stearothermophilus, Geobacillus stearothermophilus T-6, Halalkalibacterium halodurans, Mesorhizobium loti, Sinorhizobium meliloti, Streptomyces coelicolor, Streptomyces lividans, Streptomyces lividans 66 1326
Manually annotated by BRENDA team
Hvel, K.; Shallom, D.; Niefind, K.; Belakhov, V.; Shoham, G.; Baasov, T.; Shoham, Y.; Schomburg, D.
Crystal structure and snapshots alaong the reaction pathway of a family 51 alpha-L-arabinofuranosidase
EMBO J.
22
4922-4932
2003
Geobacillus stearothermophilus (Q9XBQ3), Geobacillus stearothermophilus T-6 (Q9XBQ3)
Manually annotated by BRENDA team
Shallom, D.; Belakhov, V.; Solomon, D.; Shoham, G.; Baasov, T.; Shoham, Y.
Detailed kinetic analysis and identification of the nucleophile in alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase
J. Biol. Chem.
277
43667-43673
2002
Geobacillus stearothermophilus (Q9XBQ3), Geobacillus stearothermophilus T-6 (Q9XBQ3)
Manually annotated by BRENDA team
Kim, K.; Kim, K.; Choi, Y.
Characterization of the arfA gene from Bacillus stearothermophilus No. 236 and its protein product, alpha-L-arabinofuranosidase
J. Microbiol. Biotechnol.
14
474-482
2004
Geobacillus stearothermophilus
-
Manually annotated by BRENDA team
Hvel, K.; Shallom, D.; Niefind, K.; Baasov, T.; Shoham, G.; Shoham, Y.; Schomburg, D.
Crystallization and preliminary X-ray analysis of a family 51 glycoside hydrolase, the alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6
Acta Crystallogr. Sect. D
59
913-915
2003
Geobacillus stearothermophilus (Q9XBQ3), Geobacillus stearothermophilus T-6 (Q9XBQ3)
Manually annotated by BRENDA team